Fisheries and Aquatic Sciences

The Korean Society of Fisheries and Aquatic Science (한국수산과학회)
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Optimized pretreatment conditions for the environmental DNA (eDNA) analysis of Apostichopus japonicus

  • Kang, Yu-An (Department of Marine Biology, Pukyong National University) ;
  • Lee, Soo Rin (Industry 4.0 Convergence Bionics Engineering, Pukyong National University) ;
  • Kim, Eun-Bi (Industry 4.0 Convergence Bionics Engineering, Pukyong National University) ;
  • Park, Sang Un (West Sea Marine Living Resources Center, Korea Fisheries Resources Agency) ;
  • Lim, Sang Min (West Sea Marine Living Resources Center, Korea Fisheries Resources Agency) ;
  • Andriyono, Sapto (Fisheries and Marine Faculty, C Campus Jl, Universitas Airlangga) ;
  • Kim, Hyun-Woo (Department of Marine Biology, Pukyong National University)
  • Received : 2022.02.19
  • Accepted : 2022.03.14
  • Published : 2022.05.31
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Abstract

A non-destructive environmental DNA protocol for the genetic analysis of sea cucumber (Apostichopus japonicus) resources DNA was established. Among the several commercial DNA extraction kits, the DNeasy® Plant Mini Kit was selected as the best choice to obtain the high-quality genomic DNAs from the mucous sea cucumber. As the temperature and incubation time increased, the amount of extracted environmental DNA was also large, but it was judged that the increased amount did not affect as much as 2-3 times. Therefore, these conditions were not considered to be the main factors to consider in actual environmental DNA extraction. However, the amount of seawater relative to the size of the sample was judged as a major consideration, and a sufficient amount of environmental DNA for analysis was secured when stored within 1 min while stirring the volume of seawater corresponding to the total sea cucumber weight (g). In securing the environmental DNA of sea cucumbers, the mortality rate of sea cucumbers in all experiments was 0, and it was judged that the effects of sea cucumbers were not significant through this treatment. Through the results of this study, sea cucumber DNA research, which has been conducted in a destructive method, can be conducted non-destructively through environmental DNA analysis. Through this study, we have secured a standard protocol that can successfully extract the sea cucumber DNA through environmental DNA. It is not only excellent in terms of time and cost of traditional DNA analysis method currently used, but it is completely non-destructive in the ecosystem of the survey area. It is believed that the system can be transformed in a way that does not affect it. However, it is thought that various standard protocols should be established considering the characteristics of each type.

Keywords

Acknowledgement

This research was funded by the Korea Fisheries Resources Agency, Korea (FIRA-RP-21-003), and partially supported by the Basic Science Research Program of the National Research Foundation of Korea (NRF), the Ministry of Education (2021R1A6A1A03039211).

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